Abstract
BackgroundTwo categories of introns are known, a common U2 type and a rare U12 type. These two types of introns are removed by distinct spliceosomes. The phylogenetic distribution of spliceosomal RNAs that are characteristic of the U12 spliceosome, i.e. the U11, U12, U4atac and U6atac RNAs, suggest that U12 spliceosomes were lost in many phylogenetic groups. We have now examined the distribution of U2 and U12 introns in many of these groups.ResultsU2 and U12 introns were predicted by making use of available EST and genomic sequences. The results show that in species or branches where U12 spliceosomal components are missing, also U12 type of introns are lacking. Examples are the choanoflagellate Monosiga brevicollis, Entamoeba histolytica, green algae, diatoms, and the fungal lineage Basidiomycota. Furthermore, whereas U12 splicing does not occur in Caenorhabditis elegans, U12 introns as well as U12 snRNAs are present in Trichinella spiralis, which is deeply branching in the nematode tree. A comparison of homologous genes in T. spiralis and C. elegans revealed different mechanisms whereby U12 introns were lost.ConclusionsThe phylogenetic distribution of U12 introns and spliceosomal RNAs give further support to an early origin of U12 dependent splicing. In addition, this distribution identifies a large number of instances during eukaryotic evolution where such splicing was lost.
Highlights
Two categories of introns are known, a common U2 type and a rare U12 type
The presence of U2 and U12 introns have been examined in a number species that we previously screened for U2 and U12 spliceosomal RNAs
The phylogenetic distribution of U12 introns is entirely consistent with the distribution of U12 spliceosomal RNAs
Summary
Two categories of introns are known, a common U2 type and a rare U12 type. These two types of introns are removed by distinct spliceosomes. Splicing of U2-type introns is catalyzed by the U2-dependent (major) spliceosome, which includes the U1, U2, U4, U5 and U6 spliceosomal RNAs as well as multiple protein factors. The U12-dependent (minor) spliceosome, responsible for the excision of the U12-type introns, is structurally similar to the U2-type spliceosome. It contains protein subunits and the U5 RNA as well as the U11, U12, U4atac, and U6atac spliceosomal RNAs that are functionally and structurally related to the U1, U2, U4 and U6 RNAs of the major spliceosome
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